DragonFly On-Line Manual Pages

obprobe(1)          DragonFly General Commands Manual (urm)         obprobe(1)

NAME
     obprobe - create electrostatic probe grid

SYNOPSIS
     obprobe [OPTIONS] type pchg filename

DESCRIPTION
     The obprobe tool creates a grid around a molecule, placing a probe atom
     with a specified atom type and partial charge at each point to calculate
     the MMFF94 energy. This can be used for docking experiments to test
     hydrogen-bond affinity, electrostatic potential, etc.  Output is sent to
     standard output using the Gaussian Cube format.

OPTIONS
     If no filename is given, obprobe will give all options including the
     example probes.

     -s stepsize
           Set the resolution of the grid (stepsize)

     -p padding
           Set the padding -- extra distance on each side of the box formed by
           the molecule.

     type  MMFF94 atom type

     pchg  MMFF94 partial charge

EXAMPLES
     Probe the file pyridines.sdf using a carbonyl oxygen -- a hydrogen bond
     acceptor with partial charge -0.57:
           obprobe 7 -0.57 pyridines.sdf

     Probe the file pyridines.sdf using a phenyl carbon atom -- a hydrophobic
     atom with no partial charge:
           obprobe 37 0.0 pyridines.sdf

SEE ALSO
     babel(1).

     The web pages for Open Babel can be found at: <http://openbabel.org/>

AUTHORS
     The obprobe program was contributed by Tim Vandermeersch.

     Open Babel is developed by a cast of many, including currrent maintainers
     Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who
     have contributed fixes and additions.  For more contributors to Open
     Babel, see <http://openbabel.org/wiki/THANKS>

COPYRIGHT
     Copyright (C) 2006-2008 by Tim Vandermeersch
     Some portions Copyright (C) 2004-2008 by Geoffrey R. Hutchison and other
     contributors.

      This program is free software; you can redistribute it and/or modify it
     under the terms of the GNU General Public License as published by the
     Free Software Foundation version 2 of the License.

      This program is distributed in the hope that it will be useful, but
     WITHOUT ANY WARRANTY; without even the implied warranty of
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
     Public License for more details.

Open Babel 2.2                   July 4, 2008                   Open Babel 2.2